File formats
Slide images
PNG / JPEG
Standard raster images. Best for local development and region-of-interest captures.
TIFF / OME-TIFF
Standard pathology scan formats. OME-TIFF preserves microscopy metadata including pixel size when embedded.
Whole-slide scanner formats
| Format | Extension | Library |
|---|---|---|
| Aperio SVS | .svs | OpenSlide |
| Hamamatsu NDPI | .ndpi | OpenSlide |
| 3DHISTECH MRXS | .mrxs | OpenSlide |
OpenSlide must be installed in the biochem environment for WSI decoder support.
Annotations
GeoJSON
Standard GeoJSON FeatureCollection with polygon or multipolygon geometries. Each feature should include a label or classification property for region naming.
QuPath exports
GeoJSON exports from QuPath follow the same import path. Region properties map to annotation labels in the viewer.
Import via POST /pathology/slides/{id}/annotations/import.
Sample metadata CSV (planned)
| Column | Required | Purpose |
|---|---|---|
external_id | Yes | Sample identifier |
diagnosis, tumor_grade, stage, treatment, response_status | No | Clinical metadata |
group_label, timepoint | No | Cohort comparison fields |
Artifact outputs
Pipeline results under data/pathology/artifacts/{run_id}/:
| Artifact | Contents |
|---|---|
tissue_mask.png | Binary tissue foreground |
tissue_regions.json | Region bounding boxes and labels |
cell_overlay.png | Segmentation visualization |
cells.json | Cell centroids, areas, confidence |
density_heatmap.png | Spatial density map |
cell_spatial_metrics.csv | Per-cell spatial measurements |
region_metrics.json | Compartment-level statistics |
Tile pyramids live under data/pathology/tiles/{slide_id}/.
Size guidance
| Image type | Approx. size |
|---|---|
| Region PNG (640×480) | < 1 MB |
| OME-TIFF region scan | 10–100 MB |
| Full WSI (40× H&E) | 1–5 GB |
Large WSI files are processed on the server with tile-first architecture. The frontend never loads full-resolution slides into memory.
Spatial transcriptomics
Visium, Xenium, and MERFISH data formats are handled by the Computational Biology area. Pathology provides tissue morphology overlays and region context — not duplicate spatial omics ingestion.